Can Machine Learning be applied to decipher the script of lost ancient languages?
I would guess no, because if the language is unknown (no data available on it), then we would not have training data with which the machine learning algorithm could learn from.

If it is related to some known language, then some statistical analysis can lead to a guess at decipherment (assuming certain similarities among the two languages).

If interested on general language decipherment, see the following where they decipher scripts using available information on the language of interest: http://www.aclweb.org/anthology/W99-0906. They utilize the Expectation Maximization algorithm. 

I'm sure more google searching can lead to other examples that use machine learning algorithms, but they would most likely have some known information or a body of assumptions to make our problem scope easier.